GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Carboxydothermus pertinax Ug1

Best path

livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB

Rules

Overview: Leucine degradation in GapMind is based on MetaCyc pathway L-leucine degradation I, via branched alpha-keto acid dehydrogenase (link). Other pathways for are not included here because they are not linked to sequence (link) or do not result in carbon incorporation.

39 steps (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) cpu_RS01320 cpu_RS01325
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) cpu_RS01325 cpu_RS11745
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) cpu_RS01340 cpu_RS13285
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) cpu_RS01335
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) cpu_RS01330
ilvE L-leucine transaminase cpu_RS05005 cpu_RS03310
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA cpu_RS03820 with cpu_RS03815
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB cpu_RS03825 cpu_RS08605
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
liuA isovaleryl-CoA dehydrogenase cpu_RS02525 cpu_RS11860
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit cpu_RS07800 cpu_RS04525
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit cpu_RS07795 cpu_RS01750
liuC 3-methylglutaconyl-CoA hydratase cpu_RS10860 cpu_RS10405
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase cpu_RS10435 cpu_RS10425
atoB acetyl-CoA C-acetyltransferase cpu_RS10880 cpu_RS10845
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP cpu_RS09910 cpu_RS09015
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2 cpu_RS11915
bcaP L-leucine uptake transporter BcaP cpu_RS07250
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT cpu_RS07350
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component cpu_RS02370
natA L-leucine ABC transporter, ATPase component 1 (NatA) cpu_RS01325 cpu_RS01320
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) cpu_RS01335
natE L-leucine ABC transporter, ATPase component 2 (NatE) cpu_RS01320 cpu_RS01325
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB cpu_RS03820

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory